Bio Sequtils, Protparam Useage Inquiry

Question

[Jesse]

I'm trying to use the ProtParamData module, but am receiving: AttributeError: 'Seq' object has no attribute 'islower' in reference to this function of the class Protein Analysis

def __init__(self, ProtSequence):
        if ProtSequence.islower():
            self.sequence = Seq(ProtSequence.upper(), IUPAC.protein)
        else:
            self.sequence = Seq(ProtSequence, IUPAC.protein)

How can I use this module/bypass this error? Thanks

[Brad Chapman]

The ProteinAnalysis class takes a string as an argument, instead of a Seq object. If you post your usage, we may be able to offer additional suggestions.

[Peter]

Although it may make sense to allow for a Seq object as well...

Answer 1

[Hamish]

An example of the usage of the ProteinAnalysis class can be found in the documentation for the Bio.SeqUtils.ProtParam module: http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-module.html